Openings

PhD positions:

PhD position 1. Molecular dynamics of phase separation-controlled gene transcription in leukemia.

Description: Acute myeloid leukemia (AML) is a genetic disease in which gene mutations accumulate in hematopoietic stem cells thereby disturbing normal blood cell development. AML is extremely difficult to treat, and better treatment options are urgently needed. AML mutations are typically found in a broad range of signaling molecules resulting in aberrant transcriptional programs that drive leukemic transformation. A better understanding of derailed signaling in AML patients is key to developing more effective treatment strategies. Recent findings indicate that transcription is not only a biochemical, but also a biophysical process: spatial localization plays a key role during which all transcriptional components, promoters and enhancers are brought together in so-called transcriptional condensates (TCs), assemblies formed by the propensity of various transcriptional regulators to phase separate at the chromatin. The biophysical process of phase separation is predominantly driven by proteins that are intrinsically disordered (IDPs), i.e., do not have a clear predefined structure. We and others have recently identified that several intrinsically disordered leukemic oncogenes might be initiators of the formation of TCs through phase separation.

These exciting observations bring together the biophysical mechanism of phase separation and the cell-biological process of oncogenic transcription. In this proposal we aim to discover how these oncogenic TCs are formed and mis-regulate gene transcription. The overarching aim of this project, using molecular dynamics simulations, is to develop a comprehensive roadmap of leukemic IDPs, unravel the composition and function of phase separation-controlled leukemic transcriptional condensates, and investigate whether interfering with their function and/or formation will provide alternative treatment strategies for patients with AML. We anticipate that our studies will not only provide important fundamental insights but also provide better therapeutic options for AML patients.

Requested skills PhD 1: We look for a candidate with a master’s degree in (bio)physics, (bio)chemistry or a related field, with a strong interest in molecular dynamics simulations. The project will entail programming (scripting, Python etc.), handling big data and carrying out all-atom and coarse-grained molecular dynamics simulations on high-performance super-computers. We expect excellent writing and speaking/presentation skills in English. This project will be carried out in close collaboration with an experimental PhD student that will start at the same time, so good team working skills are required.

PhD position 2. Computational modelling of synthetic living systems

Description: At the origin of life, chemical reaction networks of prebiotic compounds played an essential role. These networks likely began relatively simple but grew in complexity over time, forming dynamic molecular structures capable of essential functions of life such as self-replication, metabolism, and compartmentalization. Our understanding of how these functions emerged from prebiotic building blocks and their reactivity in different environmental conditions is only starting to unfold. While most biomolecules can now be synthesized under prebiotic conditions, organizing them into a self-sustaining, thermodynamically out-of-equilibrium living system poses a major challenge. This project aims to generate a synthetic living system that features multiple functions of life by modelling the emergence of metabolism and compartmentalization using a simple out-of-equilibrium peptide-based self-replicating system as a starting point.

The PRELIFE consortium

This project is part of the PRELIFE consortium (15 PhD projects): The origin of life remains one of the greatest mysteries in science. While many theories have been proposed, no single explanation has yet gained universal agreement. That’s where the PRELIFE consortium comes in. PRELIFE unites experts across a wide range of disciplines from astronomy, biology, chemistry, computer science, earth and planetary sciences, education, mathematics, to physics. Together we will explore two fundamental questions: How did life emerge on Earth, and how common are the conditions elsewhere in the universe? 

Requested skills PhD 2: We are looking for a candidate with a master’s degree in (applied) mathematics, (bio)physics, (bio)chemistry, biomedical / life-sciences or a related field with a strong interest in computational modelling. The project will entail programming (scripting, Python etc.), solving coupled differential equations and carrying out molecular dynamics simulations on high-performance super-computers.

You will be employed at the Free university in Amsterdam (VU). You will be supervised by Bob Planqué (VU) and Patrick Onck (RUG). The first two years you will work in Groningen; the second two years in Amsterdam.

The preferred starting date is 15.07.2025

What we offer for both PhD positions:

- full-time contract for 4 years
- a monthly salary of €  2901 gross in the first year to a maximum of € 3707 gross per month in the final year (PhD salary scale), based on a full-time position
- a holiday allowance of 8% gross annual income and an 8.3% year-end bonus
- preferred starting date in summer 2025

Contact and application:
For PhD position 1: send your CV to Prof.dr.ir. P.R. Onck (p.r.onck rug.nl or http://www.rug.nl/staff/p.r.onck/index).
For PhD position 2: send your CV to Prof.dr.ir. P.R. Onck (p.r.onck rug.nl or http://www.rug.nl/staff/p.r.onck/index) and Dr. B. Planque (r.planque@vu.nl or https://www.few.vu.nl/~rplanque)

Upcoming PhD/Postdoc positions

We also have 2 openings for PhD/postdoc positions to work on Transport through the nuclear pore complex. A more detailled description will follow soon.